Greg,
Thank you for looking into this. On the tensorflow side, people are pushing the anaconda team to support Python 3.6. No problems with rdkit and Python 3.6. I appreciate the ease of just typing "conda install" or "conda update" and I haven't actually tried alternates for getting tensorflow running in anaconda3. Both you and the anaconda team are a real boon to the scientific community, I don't want to complain!
Jon T. Swanson, Ph.D.
ChemModeling, LLC
Suite 101, 500 Huber Park Ct.
Weldon Spring, MO 63304
(636) 329-0300
-------- Original Message --------
Subject: Re: [Rdkit-discuss] Getting rdkit to work with Anaconda Python
3.5.x
From: Greg Landrum < [email protected]>
Date: Mon, July 23, 2018 6:57 am
To: [email protected]
Cc: RDKit Discuss < [email protected]>
Well, I think I figured it out: there's a problem with the python 3.5 boost build on windows that is provided by the anaconda team: it actually depends on python 3.6.
If the silence from the anaconda team continues, I can try to do an rdkit-channel build of the relevant conda packages, but I would very much like to avoid that if possible.
-greg
Hi Jon,
I can reproduce this problem locally, which is a bit strange since the tests passed before I uploaded the 2018.03.1 build. I will take a look and see if I can figure out what's going on.
In the meantime, it may work to try installing the rdkit from the conda-forge channel: "conda install -c conda-forge rdkit" The conda-forge builds are quite useful, but they do introduce a different set of dependencies and may not work for you.
-greg
I downgraded rdkit to 2017.09 and that resolved the problem. I had already downgraded Python to 3.5.4. You need to do both of these downgrades. First downgrade Python, then downgrade rdkit. Now everything is working. Including all the other stuff like pandas, jupyter, etc.
If I just want the latest rdkit, it works fine with the Anaconda3 Python 3.6. I have scripts that want to use both rdkit and tensorflow, however.
Jon T. Swanson, Ph.D.
ChemModeling, LLC
Suite 101, 500 Huber Park Ct.
Weldon Spring, MO 63304
(636) 329-0300
-------- Original Message -------- Subject: [Rdkit-discuss] Getting rdkit to work with Anaconda Python 3.5.x From: < [email protected]> Date: Sun, July 22, 2018 2:08 pm To: "RDKit Discuss" < [email protected]> Hi,
Does anyone have a magic recipe for getting rdkit to work with python 3.5 in Anaconda3?
I am trying to create a conda environment that will allow me to run rdkit and tensorflow.
I have Anaconda3 installed (Windows 10). That installs Python 3.6 by default.
So I created an environment for Python 3.5 (which is what tensorflow wants)
conda create -n py35 python=3.5 activate py35 conda install -c anaconda tensorflow conda install -c rdkit rdkit
both install.
Tensorflow works, but
from rdkit import Chem
gives
Fatal Python error: PyThreadState_Get: no current thread
I read some old posts on this and downgraded Python to 3.5.4, then 3.5.3 and finally 3.5.0. I've tried removing and recreating the environment. Same error. I've tried just installing rdkit. Same error.
I've spent all day on this, I'm hoping someone has tried this and has a solution!
Is there a specific rdkit version I should try? People must have run rdkit in Anaconda with Python 3.5 in the past.
Jon T. Swanson, Ph.D.
ChemModeling, LLC
Suite 101, 500 Huber Park Ct.
Weldon Spring, MO 63304
(636) 329-0300 |
------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss |
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
|
